QTL mapping of resistance to race Ug99 of Puccinia graminis f. sp. tritici in durum wheat (Triticum durum Desf.)

Stem rust caused by Puccinia graminis f. sp. tritici was historically one of the most destructive diseases of wheat worldwide. The evolution and rapid migration of race TTKSK (Ug99) and derivatives, first detected in Uganda in 1999, are of international concern due to the virulence of these races to widely used stem rust resistance genes. In attempts to identify quantitative trait loci (QTL) linked with resistance to stem rust race Ug99, 95 recombinant inbred lines that were developed from a cross between two durum wheat varieties, Kristal and Sebatel, were evaluated for reaction to stem rust. Seven field trials at two locations were carried out in main and off seasons. In addition to the natural infection, the nursery was also artificially inoculated with urediniospores of stem rust race Ug99 and a mixture of locally collected stem rust urediniospores. A genetic map was constructed based on 207 simple sequence repeat (SSR) and two sequence tagged site loci. Using composite interval mapping, nine QTL for resistance to stem rust were identified on chromosomes 1AL, 2AS, 3BS, 4BL, 5BL, 6AL 7A, 7AL and 7BL. These results suggest that durum wheat resistance to stem rust is oligogenic and that there is potential to identify previously uncharacterized resistance genes with minor effects. The SSR markers that are closely linked to the QTL can be used for marker-assisted selection for stem rust resistance in durum wheat.     

Prevalence of Trachoma at Sub-District Level in Ethiopia: Determining When to Stop Mass Azithromycin Distribution

Background

To eliminate blinding trachoma, the World Health Organization emphasizes implementing the SAFE strategy, which includes annual mass drug administration (MDA) with azithromycin to the whole population of endemic districts. Prevalence surveys to assess impact at the district level are recommended after at least 3 years of intervention. The decision to stop MDA is based on a prevalence of trachomatous inflammation follicular (TF) among children aged 1–9 years below 5% at the sub-district level, as determined by an additional round of surveys limited within districts where TF prevalence is below 10%. We conducted impact surveys powered to estimate prevalence simultaneously at the sub-district and district in two zones of Amhara, Ethiopia to determine whether MDA could be stopped.

Methodology

Seventy-two separate population-based, sub-district surveys were conducted in 25 districts. In each survey all residents from 10 randomly selected clusters were screened for clinical signs of trachoma. Data were weighted according to selection probabilities and adjusted for correlation due to clustering.

Principal Findings

Overall, 89,735 residents were registered from 21,327 households of whom 72,452 people (80.7%) were examined. The prevalence of TF in children aged 1–9 years was below 5% in six sub-districts and two districts. Sub-district level prevalence of TF in children aged 1–9 years ranged from 0.9–76.9% and district-level from 0.9–67.0%. In only one district was the prevalence of trichiasis below 0.1%.

Conclusions/Significance

The experience from these zones in Ethiopia demonstrates that impact assessments designed to give a prevalence estimate of TF at sub-district level are possible, although the scale of the work was challenging. Given the assessed district-level prevalence of TF, sub-district-level surveys would have been warranted in only five districts. Interpretation was not as simple as stopping MDA in sub-districts below 5% given programmatic challenges of exempting sub-districts from a highly regarded program and the proximity of hyper-endemic sub-districts.     

Chloroplast DNA haplotype diversity and postglacial recolonization of Hagenia abyssinica (Bruce) J.F. Gmel. in Ethiopia

We investigated genetic variation of 273 individuals from 25 populations of the monotypic species Hagenia abyssinica (Rosaceae) from the highlands of Ethiopia at three chloroplast microsatellite loci. The objectives were to infer the factors that shaped the genetic structure and to reconstruct the recolonization history of the species. Six haplotypes that were phylogenetically grouped into two lineages were identified. Homology of the three loci to the respective regions of the chloroplast genome was confirmed by sequencing. The chloroplast haplotypes found in Hagenia showed a clear pattern of congruence between their geographical distribution and genealogical relationships. A very low haplotype diversity within populations (h _S = 0.079, v _S = 0.058) and a very high population differentiation (G _ST = 0.899, N _ST = 0.926) was observed, reflecting very low mixing between recolonizing lineages. Restricted gene flow through seeds, rare long-distance dispersal, contiguous range expansion and mutation shaped the genetic structure of Hagenia. Fossil pollen records suggested that the trend of postglacial recolonization of Hagenia was first in the south and latter went to the north in Ethiopia.     

Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene

MYH9 has been proposed as a major genetic risk locus for a spectrum of nondiabetic end stage kidney disease (ESKD). We use recently released sequences from the 1000 Genomes Project to identify two western African-specific missense mutations (S342G and I384M) in the neighboring APOL1 gene, and demonstrate that these are more strongly associated with ESKD than previously reported MYH9 variants. The APOL1 gene product, apolipoprotein L-1, has been studied for its roles in trypanosomal lysis, autophagic cell death, lipid metabolism, as well as vascular and other biological activities. We also show that the distribution of these newly identified APOL1 risk variants in African populations is consistent with the pattern of African ancestry ESKD risk previously attributed to MYH9. Mapping by admixture linkage disequilibrium (MALD) localized an interval on chromosome 22, in a region that includes the MYH9 gene, which was shown to contain African ancestry risk variants associated with certain forms of ESKD (Kao et al. 2008; Kopp et al. 2008). MYH9 encodes nonmuscle myosin heavy chain IIa, a major cytoskeletal nanomotor protein expressed in many cell types, including podocyte cells of the renal glomerulus. Moreover, 39 different coding region mutations in MYH9 have been identified in patients with a group of rare syndromes, collectively termed the Giant Platelet Syndromes, with clear autosomal dominant inheritance, and various clinical manifestations, sometimes also including glomerular pathology and chronic kidney disease (Kopp 2010; Sekine et al. 2010). Accordingly, MYH9 was further explored in these studies as the leading candidate gene responsible for the MALD signal. Dense mapping of MYH9 identified individual single nucleotide polymorphisms (SNPs) and sets of such SNPs grouped as haplotypes that were found to be highly associated with a large and important group of ESKD risk phenotypes, which as a consequence were designated as MYH9-associated nephropathies (Bostrom and Freedman 2010). These included HIV-associated nephropathy (HIVAN), primary nonmonogenic forms of focal segmental glomerulosclerosis, and hypertension affiliated chronic kidney disease not attributed to other etiologies (Bostrom and Freedman 2010). The MYH9 SNP and haplotype associations observed with these forms of ESKD yielded the largest odds ratios (OR) reported to date for the association of common variants with common disease risk (Winkler et al. 2010). Two specific MYH9 variants (rs5750250 of S-haplotype and rs11912763 of F-haplotype) were designated as most strongly predictive on the basis of Receiver Operating Characteristic analysis (Nelson et al. 2010). These MYH9 association studies were then also extended to earlier stage and related kidney disease phenotypes and to population groups with varying degrees of recent African ancestry admixture (Behar et al. 2010; Freedman et al. 2009a, b; Nelson et al. 2010), and led to the expectation of finding a functional African ancestry causative variant within MYH9. However, despite intensive efforts including re-sequencing of the MYH9 gene no suggested functional mutation has been identified (Nelson et al. 2010; Winkler et al. 2010). This led us to re-examine the interval surrounding MYH9 and to the detection of novel missense mutations with predicted functional effects in the neighboring APOL1 gene, which are significantly more associated with ESKD than all previously reported SNPs in MYH9.     

Rapid effects of progesterone on ciliary beat frequency in the mouse fallopian tube

Background  

The physiological regulation of ciliary beat frequency (CBF) within the fallopian tube is important for controlling the transport of gametes and the fertilized ovum. Progesterone influences gamete transport in the fallopian tube of several mammalian species. In fallopian tubes isolated from cows, treatment with 20 micromolar progesterone caused a rapid reduction of the tubal CBF. The aims of this study were to establish methodology for studying fallopian tube CBF in the mouse, as it is an important model species, and to investigate if progesterone rapidly affects the CBF of mice at nM concentrations.     

Prevalence of intestinal parasitic infection and its associated factors among primary school students in Ethiopia: A systematic review and meta-analysis

IntroductionIntestinal parasitic infection are a major public health concern affecting both children and adolescents in Ethiopia. The aim of this systematic review and meta-analysis was to determine pooled prevalence and associated factors of intestinal parasitic infection in this target group.MethodWe systematically retrieved available articles on the prevalence of intestinal parasitic infection following database searches using PubMed, Scopus, Cochrane Library, and Science Direct between March 1 and May 27, 2020. Two authors independently extracted all relevant data using a standardized Microsoft Excel data extraction form. Heterogeneity among included studies was assessed with the Higgins I² tests. The pooled estimates and associated factors were assessed with a random-effects model using Stata/se Version 14.ResultWe retrieved 30 eligible articles with a pooled sample size of 14,445 primary school children with response rate of 97.8%. Entamoeba spp (16.11%), Ascaris lumbricoides (13.98%), hookworm (12.51%) and Giardia lamblia (9.98%) are the top causes of intestinal parasitic infection among primary school children in Ethiopia. The pooled prevalence for at least one intestinal parasitic infection was 46.09 (95% CI: 38.50, 53.68). Heterogeneity was assessed by doing subgroup analysis by study province/region. Thus, the highest prevalence of 66.6% (95% CI: 55.5, 77.7) occurred in Tigray region, which was followed by Southern Nations, Nationalities, and Peoples’ Region at 50.8% (95% CI: 33.1, 68.5). No latrine availability (OR = 4.39: 2.50,7.73), no fingernail hygiene (OR = 2.37: 1.67, 3.35), open defecation (OR = 1.67:1.64,4.36), no formal maternal education (OR = 2.02: 1.18,3.47), rural residence (OR = 1.88: 1.46, 2.41), no habit of wearing shoes (OR = 2.66: 1.79, 3.96), non-pipe source of drinking water (OR = 1.99: 1.42,2.76), no regular hand washing practices (OR = 3.45:1.85,6.47), and no habit of washing fruits and vegetables (OR = 1.59:1.01,2.49) were associated with parasitic infection.ConclusionsThe prevalence of intestinal parasitic infection was high (46%). Attention should be given to promoting personal hygiene, latrine utilization, wearing shoes, avoiding eating raw food, creating awareness for those mothers who lack formal education. Moreover, future research ideally will expand on the topic by conducting research in regions which have no prior research.     

Minimizing the Livelihood Trade-Offs of Natural Resource Management in the Eastern African Highlands: Policy Implications of a Project in “Creative Governance”

The highlands of Eastern Africa are characterized by high population densities and tightly coupled interactions between adjacent landscape units and users. Effective formal or informal natural resource governance is necessary to mitigate the potential negative social and environmental effects of individuals’ behavior. Yet many natural resource management and development problems that require or benefit from collective solutions remain unresolved (German et al. Environ Dev Sustain 8: 535–552, 2006a; German et al. 2006b; German et al. Q J Int Agr 47(3): 191–216, 2008). We argue that many of the more intractable problems in improving governance stem from the trade-offs that underlie them, which may include a loss of livelihood options for at least some households, leading to governance break down. Following a brief introduction to natural resource management and governance in Eastern Africa, we analyze the results of participatory by-law deliberations by distilling the restrictions proposed governance reforms pose to certain local stakeholders. We recommend that future policy for improved landscape governance couple institutional reforms with livelihood alternatives that reduce the burden of good governance on households.